svn commit: r512018 - in head/biology/trimmomatic: . files

[Jason W. Bacon]

Author: jwb
Date: Sat Sep 14 14:45:49 2019
New Revision: 512018
URL: https://svnweb.freebsd.org/changeset/ports/512018

Log:
  biology/trimmomatic: Upgrade to 0.39
  
  Add convenience script to run without knowing the location of the Java jar

Added:
  head/biology/trimmomatic/files/
  head/biology/trimmomatic/files/trimmomatic.in   (contents, props changed)
Modified:
  head/biology/trimmomatic/Makefile
  head/biology/trimmomatic/distinfo
  head/biology/trimmomatic/pkg-plist

Modified: head/biology/trimmomatic/Makefile
==============================================================================
--- head/biology/trimmomatic/Makefile	Sat Sep 14 14:26:31 2019	(r512017)
+++ head/biology/trimmomatic/Makefile	Sat Sep 14 14:45:49 2019	(r512018)
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	trimmomatic
-PORTVERSION=	0.35
+DISTVERSION=	0.39
 CATEGORIES=	biology java
 MASTER_SITES=	http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/
 DISTNAME=	Trimmomatic-${PORTVERSION}
@@ -11,17 +11,22 @@ MAINTAINER=	jwb at FreeBSD.org
 COMMENT=	Flexible read trimming tool for Illumina NGS data
 
 LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/LICENSE
 
 USES=		zip
 USE_JAVA=	yes
+
 JAVA_VERSION=	1.6+
 JAVA_RUN=	yes
 NO_BUILD=	yes
 NO_ARCH=	yes
 
+SUB_FILES=	trimmomatic
+
 do-install:
 	${INSTALL_DATA} ${WRKSRC}/trimmomatic-${PORTVERSION}.jar \
 		${STAGEDIR}${JAVAJARDIR}/trimmomatic.jar
 	cd ${WRKSRC} && ${COPYTREE_SHARE} adapters ${STAGEDIR}${DATADIR}
+	${INSTALL_SCRIPT} ${WRKDIR}/trimmomatic ${STAGEDIR}${PREFIX}/bin
 
 .include <bsd.port.mk>

Modified: head/biology/trimmomatic/distinfo
==============================================================================
--- head/biology/trimmomatic/distinfo	Sat Sep 14 14:26:31 2019	(r512017)
+++ head/biology/trimmomatic/distinfo	Sat Sep 14 14:45:49 2019	(r512018)
@@ -1,2 +1,3 @@
-SHA256 (Trimmomatic-0.35.zip) = 43b993ffa91c039b529db8334bc6aa4b0d601e69c79aaa9a1457ecd1c2c3cc69
-SIZE (Trimmomatic-0.35.zip) = 129810
+TIMESTAMP = 1568469691
+SHA256 (Trimmomatic-0.39.zip) = 2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca
+SIZE (Trimmomatic-0.39.zip) = 133596

Added: head/biology/trimmomatic/files/trimmomatic.in
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/trimmomatic/files/trimmomatic.in	Sat Sep 14 14:45:49 2019	(r512018)
@@ -0,0 +1,3 @@
+#!/bin/sh -e
+
+java -jar %%PREFIX%%/share/java/classes/trimmomatic.jar "$@"

Modified: head/biology/trimmomatic/pkg-plist
==============================================================================
--- head/biology/trimmomatic/pkg-plist	Sat Sep 14 14:26:31 2019	(r512017)
+++ head/biology/trimmomatic/pkg-plist	Sat Sep 14 14:45:49 2019	(r512018)
@@ -1,7 +1,8 @@
+bin/trimmomatic
+%%JAVAJARDIR%%/trimmomatic.jar
 %%DATADIR%%/adapters/NexteraPE-PE.fa
 %%DATADIR%%/adapters/TruSeq2-PE.fa
 %%DATADIR%%/adapters/TruSeq2-SE.fa
 %%DATADIR%%/adapters/TruSeq3-PE-2.fa
 %%DATADIR%%/adapters/TruSeq3-PE.fa
 %%DATADIR%%/adapters/TruSeq3-SE.fa
-%%JAVAJARDIR%%/trimmomatic.jar